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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattcttacttcaaacctttccaccggacatcagaatttatgactttccaatttctattctaatgcaaatgttggtattttgtgcacccag

Basic information

species Glycine max
transcript GLYMA15G13080.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13080.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 5'ss of exon 4
GGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaa--caattcttacttcaaacctttccaccggaca----tcagaatttatgactttccaatttctattctaatgcaaatgttggtattttgtgcacccag
|| |||||||||||||||||| ||| |||||| ||||| ||||| |||||| |||||||||| ||  | ||  ||||||  |  ||||| |||||||| ||| |   |  |   |  |  ||  | | |  |  | |    ||  | | |  | |||     | | |    ||    |||||    | ||| ||     |||
GGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttaccttccagctttaatgtctgcctctaataaaactccaactgtggggcttgttcttgtttcagatatctaaaatga-aatctttggtatgtgcag

upper sequence: GLYMA15G13080.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 5'ss of exon 4
GGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaac--aattcttacttca--aacctttccaccggacatcagaatttatgactttccaatttctattctaatgcaaatgttggtattttgtgcacccag-----
||||||||||||||||||||| | | ||| |||||||| || || |||||||| |||||||| || |||||  |||||||||||||||| ||||| ||||||| |  |  |  || |||   |||||| |     |   |  | ||    |  |  |||| ||  |  | ||  |  |   |  | ||||| | ||||       
GGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCATACCTACCGATTTTCACAAGCTTTAACAGAACAAAAGgtaccccagctaatatttcgtcaaccttacagtttg--gtggggatg---ggttgcccaagtttaacacaaaaacttaatgtaatgttttgggtaccccttgcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|6502372|gb|AW203745.1|AW203745
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|14012135|gb|BG727057.1|BG727057
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|10709738|gb|BF009462.1|BF009462
EST:     AATCATGTGCTCCTATCTACCAGTTGTCACAAGCTTTAATAGAACCAAAA                         GTGGCTTGATTTAATTAAACCACGGTAAGCCTCAACCTTTTCCA-TATGTG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCT-CCAATATGTG
EST: gi|15664637|gb|BI702008.1|BI702008
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAA                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAG
EST: gi|7640040|gb|AW734349.1|AW734349
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|13789346|gb|BG651937.1|BG651937
EST:     GTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: GTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
EST: gi|6072595|gb|AW101982.1|AW101982
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTTAAGACCTCTCCAATATGT
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCC-TCAG-CCTCTCCAATATGT
EST: gi|15813092|gb|BI785367.1|BI785367
EST:     AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAG                         GTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG
genomic: AATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattc ... gtgcacccagGTGGCTTGATTCAATTAAACCACGGTAGGCCTCAGCCTCTCCAATATGTGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCTATCTACCAGTTTTCACAAGCTTTAATAGAACCAAAGgtaacaattcttacttcaaacctttccaccggacatcagaatttatgactttccaatttctattctaatgcaaatgttggtattttgtgcacccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT